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PubMed2006

Microfluidic and optical systems for the on-demand generation and manipulation of single femtoliter-volume aqueous droplets.

This paper describes a fluidic and optical platform for the generation and manipulation of single femtoliter-volume aqueous droplets. Individual droplets were generated on-demand using a microfluidic chamber that confers environmental flow stability. Optical vortex traps were implemented to manipulate and transport the generated droplets, which have a lower refractive index than the immiscible medium in which the droplets are immersed and thus cannot be trapped using conventional optical tweezers. We also demonstrated the ability to shrink and increase the refractive index of the generated droplet, thereby permitting its facile fusion with another droplet using an optical tweezer. To illustrate the versatility of this platform, we have performed both fast (<1 s) and slow (>1 h) chemical reactions in these femtoliter-volume aqueous droplets.

Journal Article↗

PubMed2005

An automated method for generating analogic signals that embody the Markov kinetics of model ionic channels.

In this work we present an automated method for generating electrical signals which reflect the kinetics of ionic channels that have custom-tailored intermediate sub-states and intermediate reaction constants. The concept of our virtual single-channel waveform generator makes use of two software platforms, one for the numerical generation of single channel traces stemming from a pre-defined model and another for the digital-to-analog conversion of such numerical generated single channel traces. This technique of continuous generation and recording of the activity of a model ionic channel provides an efficient protocol to teach neophytes in the field of single-channel electrophysiology about its major phenomenological facets. Random analogic signals generated by using our technique can be successfully employed in a number of applications, such us: assisted learning of the single-molecule kinetic investigation via electrical recordings, impedance spectroscopy, the evaluation of linear frequency response of neurons and the study of stochastic resonance of ion channels.

Animals↗

PubMed2005

Fluorescent amplifying recognition for DNA G-quadruplex folding with a cationic conjugated polymer: a platform for homogeneous potassium detection.

Single-stranded DNA with G-rich sequences can fold into secondary structures, G-quadruplexes, via intramolecular hydrogen-bonding interactions. This conformational change can be detected by a homogeneous assay method based on fluorescence resonance energy transfer (FRET) from a water-soluble cationic conjugated polymer (CCP) to a fluorescein chromophore labeled at the terminus of the G-quadruplex DNA. The space charge density around the DNA controls the efficiency of FRET from the CCP to the fluorescein. The higher FRET efficiency for the CCP/G-quadruplex pair is correlated to the stronger electrostatic interactions between the more condensed G-quadruplex and the CCP in comparison to the CCP/ssDNA pair. Since the potassium ion can specifically bind to the G-quadruplex DNA, the G-quartet-DNA/CCPs assembly can also be used as a platform to sense the potassium ion in water with high selectivity and sensitivity.

Biosensing Techniques↗

PubMed1986

Dynamic posture analysis of Spacelab-1 crew members.

Dynamic posture testing was conducted on the science crew of the Spacelab-1 mission on a single axis linear motion platform. Tests took place in pre- and post-flight sessions lasting approximately 20 min each. The pre-flight tests were widely spaced over the several months prior to the mission while the post-flight tests were conducted over the first, second, fourth, and sixth days after landing. Two of the crew members were also tested on the day of landing. Consistent with previous postural testing conducted on flight crews, these crew members were able to complete simple postural tasks to an acceptable level even in the first few hours after landing. Our tests were designed to induce dynamic postural responses using a variety of stimuli and from these responses, evaluate subtle changes in the postural control system which had occurred over the duration of the flight. Periodic sampling post-flight allowed us to observe the time course of readaptation to terrestrial life. Our observations of hip and shoulder position, when subjected to careful analysis, indicated modification of the postural response from pre- to post-flight and that demonstrable adjustments in the dynamic control of their postural systems were taking place in the first few days after flight. For transient stimuli where the platform on which they were asked to stand quickly moved a few centimeters fore or aft then stopped, ballistic or open loop 'programs' would closely characterize the response. During these responses the desired target position was not always achieved and of equal importance not always properly corrected some 15 seconds after the platform ceased to move. The persistent observation was that the subjects had a much stronger dependence on visual stabilization post-flight than pre-flight. This was best illustrated by a slow or only partial recovery to an upward posture after a transient base-of-support movement with eyes open. Postural responses to persistent wideband pseudorandom base-of-support translation were modeled as time invarient linear systems arrived at by Kalman adaptive filter techniques. Derived model parameters such as damping factor and fundamental frequency of the closed loop system showed significant modification between pre- and post-flight. This phenomenon is best characterized by movement of the poles toward increasing stability. While pre-flight data tended to show shoulders and hips moving in phase with each other, post-flight data showed a more disjoint behavior.(ABSTRACT TRUNCATED AT 400 WORDS)

Adaptation, Physiological↗

PubMed2026

Metal-organic frameworks nanozyme-integrated portable microneedle patch for visual bacterial monitoring in meat.

Foodborne microbial contamination is a major global health concern, with conventional methods often being time-consuming and complex. Herein, we developed a novel portable biosensor by integrating microneedle patch technology and a metal-organic framework (Fe/Cu-NBDC MOF) nanozyme, enabling rapid, on-site, visual detection of bacteria in meat. The sensing system works by encapsulating aptamer-functionalized MOF nanozymes within a hydrogel patch, where their catalytic sites are initially blocked by the aptamer. In the presence of Staphylococcus aureus (S. aureus) as the target, the specific aptamer's binding to bacteria exposes numerous catalytic sites, further activating the chromogenic reaction of the tetramethylbenzidine‑hydrogen peroxide (TMB-H₂O₂) system, enabling visual detection of S. aureus. The biosensor demonstrates a detection limit of 82 CFU/mL with excellent specificity to successfully apply to commercial mutton. By integrating sampling, enrichment, and visual detection into a single compact device, this platform offers a practical, efficient solution for rapid on-site screening of foodborne pathogens.

Biosensing Techniques↗

PubMed2005

Tag/anti-tag liquid-phase primer extension array: a flexible and versatile genotyping platform.

This study demonstrates an array-based platform to genotype simultaneously single nucleotide polymorphisms (SNPs) and some short insertions/deletions (indels) by the integration of the universal tag/anti-tag (TAT) system, liquid-phase primer extension (LIPEX), and a novel two-color detection strategy on an array format (TATLIPEXA). The TAT system permits a universal chip to be used for many applications, and the LIPEX simplifies the sample preparation but improves the sensitivity significantly. More importantly, all SNPs and some short indels can be interrogated in a single reaction with only two fluorescent ddNTPs. The concept of TATLIPEXA is demonstrated for nine SNPs (eight point mutations and one single-base insertion), and genotypes obtained show a remarkable concordance rate of 100% with both DNA sequencing and restriction fragment length polymorphism. Moreover, TATLIPEXA is able to provide quantitative information on allele frequency in pooled DNA samples, which could serve as a rapid screening tool for SNPs associated with diseases.

Coronary Artery Disease↗

PubMed2003

Broadband coupling into a single-mode, electroactive integrated optical waveguide for spectroelectrochemical analysis of surface-confined redox couples.

A single-mode, electroactive waveguiding platform capable of measuring spectroelectrochemical responses of surface-adsorbed redox-active molecules over a broad spectral bandwidth has been created. This new planar waveguide spectrometer is a combination of the previously developed electroactive integrated optical waveguide (EA-IOW; Dunphy, D. R.; Mendes, S. B.; Saavedra, S. S.; Armstrong, N. R. Anal. Chem. 1997, 69, 3086-3094) with a recently reported simplified approach to broadband coupling (Bradshaw, J. T.; Mendes, S. B.; Saavedra, S. S. Anal. Chem. 2002, 74, 1751-1759). With the use of a commercially available prism as an incoupling element, the EA-IOW can now guide visible light from at least 500 to 700 nm, improving upon its previously demonstrated monochromatic nature. Coupling profiles of various laser lines along with transmission spectra of narrow band-pass filters at various potentials are used to demonstrate the optical characteristics of this broadband EA-IOW and to compare its response to that of a conventional transmission instrument. Assessment of spectral resolution, performed by measuring the fwhm of various laser lines, ranges from 0.6 to 0.8. To demonstrate the capabilities of this technology, we show the acquisition of absorbance spectra of two different adsorbates, cytochrome c and ferrocenedicarboxylic acid, as a function of applied potential. Subtleties in the redox chemistries of adsorbed molecules, which were difficult to monitor with a monochromatic waveguide, are readily apparent when using the broadband coupling scheme.

Electrochemistry↗

PubMed2005

Hourly monitoring of circulating CD34+ cells to optimize timing of autologous apheresis in pediatric patients.

In order to increase the CD34+ cell yield in children undergoing autologous stem cell transplantation, the optimum time of apheresis after G-CSF administration has still to be found. We prospectively studied the mobilization of CD34+ cells and white blood cells in the peripheral blood (PB) of 20 pediatric patients before leukapheresis. The monitoring schedule covered 12 h, with blood samples taken before and at 2, 4, 5, 6, 7, 8, 10 and 12 h after G-CSF administration when 10 CD34+ cells/mul were reached. CD34+ cells were measured by flow cytometric analysis both in the single- and dual-platform setting. Two different patterns of mobilization (POM) emerged: 12 patients showed an increase in CD34+ cells in PB during the first 4 h after G-CSF (POM I), while eight patients had an initial decrease of CD34+ cells. However, all patients together showed a significant increase of CD34+ cells about 10 h after G-CSF administration. Further studies with more patients, using an enhanced monitoring schedule will be required to refine the results.

Adolescent↗

PubMed1996

Native 3D structure of eukaryotic 80s ribosome: morphological homology with E. coli 70S ribosome.

A three-dimensional reconstruction of the eukaryotic 80S monosome from a frozen-hydrated electron microscopic preparation reveals the native structure of this macromolecular complex. The new structure, at 38A resolution, shows a marked resemblance to the structure determined for the E. coli 70S ribosome (Frank, J., A. Verschoor, Y. Li, J. Zhu, R.K. Lata, M. Radermacher, P. Penczek, R. Grassucci, R.K. Agrawal, and Srivastava. 1996b. In press; Frank, J., J. Zhu, P. Penczek, Y. Li, S. Srivastava ., A. Verschoor, M. Radermacher, R. Grassucci, R.K. Lata, and R. Agrawal. 1995. Nature (Lond.).376:441-444.) limited to a comparable resolution, but with a number of eukaryotic elaborations superimposed. Although considerably greater size and intricacy of the features is seen in the morphology of the large subunit (60S vs 50S), the most striking differences are in the small subunit morphology (40S vs 30S): the extended beak and crest features of the head, the back lobes, and the feet. However, the structure underlying these extra features appears to be remarkably similar in form to the 30S portion of the 70S structure. The intersubunit space also appears to be strongly conserved, as might be expected from the degree of functional conservation of the ribosome among kingdoms (Eukarya, Eubacteria, and Archaea). The internal organization of the 80S structure appears as an armature or core of high-density material for each subunit, with the two cores linked by a single bridge between the platform region of the 40S subunit and the region below the presumed peptidyltransferase center of the 60S subunit. This may be equated with a close contact of the 18S and 28S rRNAs in the translational domain centered on the upper subunit:subunit interface.

Bacterial Proteins↗

PubMed2005

Exon array CGH: detection of copy-number changes at the resolution of individual exons in the human genome.

The development of high-throughput screening methods such as array-based comparative genome hybridization (array CGH) allows screening of the human genome for copy-number changes. Current array CGH strategies have limits of resolution that make detection of small (less than a few tens of kilobases) gains or losses of genomic DNA difficult to identify. We report here a significant improvement in the resolution of array CGH, with the development of an array platform that utilizes single-stranded DNA array elements to accurately measure copy-number changes of individual exons in the human genome. Using this technology, we screened 31 patient samples across an array containing a total of 162 exons for five disease genes and detected copy-number changes, ranging from whole-gene deletions and duplications to single-exon deletions and duplications, in 100% of the cases. Our data demonstrate that it is possible to screen the human genome for copy-number changes with array CGH at a resolution that is 2 orders of magnitude higher than that previously reported.

Exons↗

PubMed2006

Structural variants: changing the landscape of chromosomes and design of disease studies.

The near completeness of human chromosome sequences is facilitating accurate characterization and assessment of all classes of genomic variation. Particularly, using the DNA reference sequence as a guide, genome scanning technologies, such as microarray-based comparative genomic hybridization (array CGH) and genome-wide single nucleotide polymorphism (SNP) platforms, have now enabled the detection of a previously unrecognized degree of larger-sized (non-SNP) variability in all genomes. This heterogeneity can include copy number variations (CNVs), inversions, insertions, deletions and other complex rearrangements, most of which are not detected by standard cytogenetics or DNA sequencing. Although these genomic alterations (collectively termed structural variants or polymorphisms) have been described previously, mainly through locus-specific studies, they are now known to be more global in occurrence. Moreover, as just one example, CNVs can contain entire genes and their number can correlate with the level of gene expression. It is also plausible that structural variants may commonly influence nearby genes through chromosomal positional or domain effects. Here, we discuss what is known of the prevalence of structural variants in the human genome and how they might influence phenotype, including the continuum of etiologic events underlying monogenic to complex diseases. Particularly, we highlight the newest studies and some classic examples of how structural variants might have adverse genetic consequences. We also discuss why analysis of structural variants should become a vital step in any genetic study going forward. All these progresses have set the stage for a golden era of combined microscopic and sub-microscopic (cytogenomic)-based research of chromosomes leading to a more complete understanding of the human genome.

Chromosomes↗

PubMed2005

Novel multipurpose methodology for detection of mycobacteria in pulmonary and extrapulmonary specimens by smear microscopy, culture, and PCR.

A novel, robust, reproducible, and multipurpose universal sample processing (USP) methodology for highly sensitive smear microscopy, culturing on solid and liquid media, and inhibition-free PCR which is suitable for the laboratory diagnosis of both pulmonary and extrapulmonary tuberculosis (TB) has been developed. This method exploits the chaotropic properties of guanidinium hydrochloride for sample processing and involves incubating the specimen with USP solution, concentrating bacilli by centrifugation, and using the processed specimen for smear microscopy, culture, and PCR. The detection limit for acid-fast bacilli in spiked sputum by smear microscopy is approximately 300 bacilli per ml of specimen. USP solution-treated specimens are fully compatible with culturing on solid and liquid media. High-quality, PCR-amplifiable mycobacterial DNA can be isolated from all types of clinical specimens processed with USP solution. The method has been extensively validated with both pulmonary and extrapulmonary specimens. Furthermore, the USP method is also compatible with smear microscopy, culture, and PCR of mycobacteria other than tubercle bacilli. In summary, the USP method provides smear microscopy, culture, and nucleic acid amplification technologies with a single sample-processing platform and, to the best of our knowledge, is the only method of its kind described to date. It is expected to be useful for the laboratory diagnosis of TB and other mycobacterial diseases by conventional and modern methods.

Bacteriological Techniques↗

PubMed2005

Comparison of normalization methods for CodeLink Bioarray data.

BACKGROUND: The quality of microarray data can seriously affect the accuracy of downstream analyses. In order to reduce variability and enhance signal reproducibility in these data, many normalization methods have been proposed and evaluated, most of which are for data obtained from cDNA microarrays and Affymetrix GeneChips. CodeLink Bioarrays are a newly emerged, single-color oligonucleotide microarray platform. To date, there are no reported studies that evaluate normalization methods for CodeLink Bioarrays. RESULTS: We compared five existing normalization approaches, in terms of both noise reduction and signal retention: Median (suggested by the manufacturer), CyclicLoess, Quantile, Iset, and Qspline. These methods were applied to two real datasets (a time course dataset and a lung disease-related dataset) generated by CodeLink Bioarrays and were assessed using multiple statistical significance tests. Compared to Median, CyclicLoess and Qspline exhibit a significant and the most consistent improvement in reduction of variability and retention of signal. CyclicLoess appears to retain more signal than Qspline. Quantile reduces more variability than Median in both datasets, yet fails to consistently retain more signal in the time course dataset. Iset does not improve over Median in either noise reduction or signal enhancement in the time course dataset. CONCLUSION: Median is insufficient either to reduce variability or to retain signal effectively for CodeLink Bioarray data. CyclicLoess is a more suitable approach for normalizing these data. CyclicLoess also seems to be the most effective method among the five different normalization strategies examined.

Algorithms↗

PubMed2005

A genome scan for parent-of-origin linkage effects in alcoholism.

BACKGROUND: Alcoholism is a complex disease in which genomic imprinting may play an important role in its susceptibility. OBJECTIVE: To conduct a genome-wide search for loci that may have strong parent-of-origin linkage effects in alcoholism; to compare the linkage results between the microsatellites and the two single-nucleotide polymorphism (SNP) platforms. METHODS: Nonparametric linkage analyses were performed using ALLEGRO with the three sets of markers provided by the Genetic Analysis Workshop 14 for the Collaborative Study on the Genetics of Alcoholism Problem 1 data. Both sex-averaged and sex-specific genetic maps were used. We also provided a valid statistical test to determine whether the parental allele sharing differed significantly. RESULTS: Significant maternal linkage effects (paternal imprinting) were observed on chromosome 12 using either the microsatellite markers or the two SNP panels. The two SNP sets did not improve the linkage signals compared to the results from the microsatellite markers on chromosome 12. Possible paternal linkage effects (maternal imprinting) on chromosome 7 and maternal linkage effects (paternal imprinting) on chromosome 10 were found using the two SNP panels. CONCLUSION: For diseases which may have parent-of-origin effects, linkage analysis looking at parental sharing separately may reduce locus heterogeneity and increase the ability to identify that which can not be identified with usual linkage analysis.

Alcoholism↗

PubMed2006

Mutation detection in congenital long QT syndrome: cardiac channel gene screen using PCR, dHPLC, and direct DNA sequencing.

Within the field of molecular cardiac electrophysiology, the previous decade of research elucidated the fundamental genetic substrate underlying many arrhythmogenic disorders such as long QT syndrome (LQTS), catecholaminergic polymorphic ventricular tachycardia (CPVT), Andersen-Tawil syndrome, Brugada Syndrome, and Timothy syndrome. In addition, the genetic basis for cardiomyopathic processes vulnerable to sudden arrhythmic death-hypertrophic cardiomyopathy, dilated cardiomyopathy, and arrhythmogenic right ventricular cardiomyopathy-are understood now in greater detail. The majority of congenital LQTS is understood as a primary cardiac channelopathy that often but not always provides evidence of its presence via a prolonged QT interval on the 12-lead surface electrocardiogram. To date, more than 300 mutations have been identified in five genes encoding key ion channel sub units involved in the orchestration of the heart's action potential. LQTS genetic testing has been performed in research laboratories over the past decade, relying on the techniques of PCR, an intermediate mutation analysis platform such as single-stranded conformation polymorphism (SSCP) or denaturing high-performance liquid chromatography (dHPLC), and subsequent direct DNA sequencing to elucidate the genetic underpinnings of this disorder. Presently, LQTS genetic testing is a clinically available molecular diagnostic test that provides comprehensive open reading frame/splice site mutational analysis via high-throughput DNA sequencing. This chapter will focus on LQTS genetic testing employing the techniques of genomic DNA isolation from peripheral blood, exon-specific PCR amplification, dHPLC hetero-duplex analysis, and direct DNA sequencing.

Animals↗

PubMed2005

The CellCard System: a novel approach to assessing compound selectivity for lead prioritization of G protein-coupled receptors.

Advances in high throughput screening technologies have led to the identification of many small molecules, "hits", with activities toward the target of interest. And, as the screening technologies become faster and more robust, the rate at which the molecules are identified continues to increase. This evolution of high throughput screening technologies has generated a significant strain on the laboratories involved with the downstream profiling of these hits using cell-based assays. The CellCard System, by enabling multiple targets and/or cell lines to be assayed simultaneously within a single well, provides a platform on which selectivity screening can be quickly and robustly performed. Here we describe two case studies using the beta-lactamase and beta-galactosidase reporter gene systems to characterize G protein-coupled receptor agonist activity. Using these examples we demonstrate how the implementation of this technology enables assay miniaturization without micro-fluidic devices as well as how the inclusion of intra-well controls can provide a means of data quality assessment within each well.

Animals↗

PubMed1995

The effects of proprioceptive ankle disk training on healthy subjects.

According to research, proprioceptive training enables injured subjects to reduce proprioceptive deficits and increase postural control. However, the effects of proprioceptive training have not been researched in healthy subjects. This study investigated the effects of Biomechanical Ankle Platform System (BAPS) training on postural sway of healthy subjects (N = 28). Subjects were pretested and posttested using the Kistler force platform while performing a single limb stance. The subjects stood on their dominant leg with the opposite hip and knee held in a self-selected position. Subjects trained the dominant leg three times per week for 10 weeks on the BAPS. Experimental subjects showed significant improvements in both the medial-lateral and anterior-posterior parameters of postural sway when compared with a control group. In conclusion, 10 weeks of proprioceptive ankle disk training significantly decreased postural sway in both the medial-lateral and anterior-posterior directions.

Adolescent↗

PubMed2006

From genome to phenome--RNAi library screening and hit characterization using signaling pathway analysis.

Comprehensive, high-throughput analysis of gene function using RNA interference (RNAi)-based screens is emerging as a significant step forward for preliminary drug-target identification. Until quite recently drug target identification depended heavily on the analysis of changes in gene expression, which in turn needed to be correlated with gene function. The promise of obtaining preliminary 'gene to phenotype' information using a single high-throughput platform is propelling major investment in this area by biotechnology and pharmaceutical companies. This review discusses recent developments in the use of RNAi library screens, and the various assay formats and techniques currently in use for data analysis downstream of such screens.

Animals↗